Known for his novels and historical works about the American Southwest, Waters's best-known novel, The Man Who Killed the Deer, was published in 1942. He was the author of 27 books, including biographies, histories, and collections of essays. His memoir, Of Time and Change (1998) was published posthumously.

When World War II broke out, Waters moved to DC to work for the Office of Inter-American Affairs, where he worked a propaganda analyst and chief content officer from 1942 to 1945.